This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.
Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Ctrl+Shift+Enter.
source("./tianfengRwrappers.R")
# plan("multiprocess",workers = 8)
human_coronary <- readRDS("human_coronary.rds")
CA_dataset1 <- readRDS("CA_dataset1.rds")
CA_dataset2 <- readRDS("CA_dataset2.rds") #已经经过分组处理了
# 提取内皮细胞亚群
ECs_list <- list(subset(CA_dataset1, idents = "Endothelial"), subset(human_coronary, idents = "Endothelial"))
ECs_list <- lapply(X = ECs_list, FUN = function(x) {
x <- NormalizeData(x)
x <- FindVariableFeatures(x, selection.method = "vst", nfeatures = 2000)
})
# 需要分析的差异基因
int_features <- SelectIntegrationFeatures(object.list = ECs_list)
# 选择合并的anchor特征
int_anchors <- FindIntegrationAnchors(object.list = ECs_list, anchor.features = int_features)
# 根据anchor合并
ECs_combined <- IntegrateData(anchorset = int_anchors)
DefaultAssay(ECs_combined) <- "integrated"
rm("ECs_list", "int_features", "int_anchors")
multi_featureplot(c("TNFRSF11B","ACTA2","CNN1","LUM"),human_coronary)
multi_featureplot(c("TNFRSF11B","ACTA2","CNN1","LUM"),CA_dataset1)
multi_featureplot(c("TNFRSF11B","ACTA2","CNN1","LUM"),CA_dataset2)
genes <- c("LGALS3","CD68","KLF4","CLDN5","VWF","ACTA2")
multi_featureplot(genes,CA_dataset2)
Dotplot(genes,CA_dataset2) # 2>5
multi_featureplot(genes,human_coronary)
Dotplot(genes,human_coronary)
cl4_marker <- FindMarkers(ds2,ident.1 = 4,logfc.threshold = 0.5, min.diff.pct = 0.3)
| | 0 % ~calculating
|++ | 3 % ~00s
|++++ | 6 % ~00s
|+++++ | 10% ~00s
|+++++++ | 13% ~00s
|+++++++++ | 16% ~00s
|++++++++++ | 19% ~00s
|++++++++++++ | 23% ~00s
|+++++++++++++ | 26% ~00s
|+++++++++++++++ | 29% ~00s
|+++++++++++++++++ | 32% ~00s
|++++++++++++++++++ | 35% ~00s
|++++++++++++++++++++ | 39% ~00s
|+++++++++++++++++++++ | 42% ~00s
|+++++++++++++++++++++++ | 45% ~00s
|+++++++++++++++++++++++++ | 48% ~00s
|++++++++++++++++++++++++++ | 52% ~00s
|++++++++++++++++++++++++++++ | 55% ~00s
|++++++++++++++++++++++++++++++ | 58% ~00s
|+++++++++++++++++++++++++++++++ | 61% ~00s
|+++++++++++++++++++++++++++++++++ | 65% ~00s
|++++++++++++++++++++++++++++++++++ | 68% ~00s
|++++++++++++++++++++++++++++++++++++ | 71% ~00s
|++++++++++++++++++++++++++++++++++++++ | 74% ~00s
|+++++++++++++++++++++++++++++++++++++++ | 77% ~00s
|+++++++++++++++++++++++++++++++++++++++++ | 81% ~00s
|++++++++++++++++++++++++++++++++++++++++++ | 84% ~00s
|++++++++++++++++++++++++++++++++++++++++++++ | 87% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++ | 90% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++ | 94% ~00s
|+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~00s
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s